研究課題

An Excel file containing information on lncRNAs probed for FM bias. The first sheet contains a README file with details on the contents of the other two sheets. The second sheet contains the list of all lncRNAs probed, a summary of their biological function, and the original source from which we extracted them. The third sheet contains the FM bias p value computed for each significantly FM biased lncRNA in each cohort. (ODS 13 kb

Additional file 2: Table S1. of Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types

List of families of driver TFs. (XLS 11 kb

Additional file 5: Table S7. of Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types

Overlap between sets of significant targets of a TF in pairs of tumor types. (XLS 69 kb

Same as in Figure 1 but for the assessment of homozygous deletions in the gliobastoma multiforme data set.

<p>All the <i>Z</i> scores obtained for the genes depicted in this figure are negative, i.e. they represent a bias towards underexpression.</p

Expression values of several known cancer genes in samples of the gliobastoma data set (log2 transformed absolute expression levels).

<p>This figure illustrates the Oncodrive-CIS analysis in different scenarios. MET and MDM4 are severely overexpressed when amplified, compared to both normal and tumor diploid samples, and they appear among the top-30 genes with larger expression change bias according to Oncodrive-CIS. However, the expression change due to CDK6 amplification was moderate and it was classified lower in the ranking list (position 138). PDGFRA was overexpressed when amplified, but the dispersion of the expression values lowered the expression impact scores calculated by Oncodrive-CIS (# 61 on the list). Thus, the two first genes should be considered as positives according to Oncodrive-CIS, whereas the remaining two genes should be considered as negatives according to our analysis criteria.</p

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Spec commercial by Liz Kosowesky for FILM105 Intro to Filmmaking.https://digitalcommons.andrews.edu/auvad-film/1023/thumbnail.jp

Additional file 2: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Supplementary methods, use cases description, Table S2. and Figures S1–S3. (PDF 6267 kb

Additional file 1: of Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Table S1. The features provided by different resources/methods and details about which of them are employed by the CGI. (XLS 21 kb